The Utah Genome Center proposes to generate a global plasmid scaffold as part of the Mouse Genome Sequencing Network. A whole genome, medium insert (12 kb), plasmid library will be constructed from Mus musculus strain C57BL/6J. High throughput automation will generate paired end sequence reads from this library using automated capillary array sequencing instruments. The goal is to sequence paired ends from approximately 3 million clones, generating 1-fold sequence coverage of the mouse genome, and 10-fold physical coverage. The sequence reads will be deposited immediately into GenBank, where they will be available for pair-wise comparison with the regional sequence contigs from the Bacterial Artificial Chromosome (BAC) working draft. The global data set that we produce will serve as a physical scaffold on the growing working draft of the mouse genome. The regionalized global data advances the BAC working draft towards finished sequence by providing more sequence coverage depth. Sequence matches from both paired ends will also order and orient working draft contigs, thus providing key information for proceeding to finished sequence. The global library will also span inter-BAC, as well as infra-BAC, working draft contigs. The sequence will be produced in an assembly line designed to reduce both personnel and labor costs in the process. This effort will contribute to completion of the mouse genome by providing a finishing resource, and will contribute to analyzing the human genome by accelerating the assembly and finishing of the mouse working draft.